- Chimera-users - RBVI Mailing Lists

Flipping the map - resolution question
by Dmitry Semchonok 14 Jul '21

14 Jul '21

Dear colleagues, I heard that flipping the map in Chimera with the command vop zflip # will decrease the resolution of the map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes> Did I understand that statement correctly? If yes, how to flip the map without losing the quality (resolution)? Thank you Sincerely, Dmitry

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Running/opening issue of chimera on HPC login node
by Rajiv Ranjan Singh 13 Jul '21

13 Jul '21

I am trying to open/run chimer; installed on a cluster login node without root privilege. Installed in Home//.local/UCSF-Chimera64-1.15rc/ Getting the following error. *login1:*~/.local/UCSF-Chimera64-1.15rc/bin $ ./chimera libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 716 Current serial number in output stream: 717 Kindly advise me to rectify this issue. Best, Rajiv Ranjan Singh

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unable to open more than one map in Chimera
by Merk, Alan (NIH/NCI) [C] 12 Jul '21

12 Jul '21

Hello, I recently updated to Catalina on my Mac and I am now not able to open more than one file at a time in Chimera. Uninstalling the program and then installing the latest version from scratch did not fix the problem. Is there any way to resolve this issue? Alan

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Users group
by Zachary Morton 09 Jul '21

09 Jul '21

Hi, My name is zach morton, I am from UC Santa Cruz and I would like to be added to the user group please. Best, Zach

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WebGL file
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

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Volume subtraction of surface area between homology model and template
by Kovacs, Nicholas (CDC/DDID/NCIRD/ID) 06 Jul '21

06 Jul '21

Hello, I have a homology model that I have made and I would like to create a visual that portrays small surfaces where there is change in the solvent accessible surface area of the homology model compared to the template structure. I am trying to use the "subtract" map from map calculation which requires volume data for the 2 structures. I have tried the following to generate volume data and then subtract the volumes, but I am getting hundreds of small surfaces all throughout the area of the molecule: molmap #1 3 molmap #2 3 volume subtract #3 #4 I know molmap is likely not the command I want to be using since I am interested in the solvent accessible surface area but I have yet to find a command that will generate a volume corresponding to the volume enclosed by the solvent accessible surface area. I would greatly appreciate it if someone could help me find a way to create 2 volumes enclosed by the solvent accessible surface area of the 2 structures in addition to correctly configuring the "volume subtract" command to get my desired output. Thank you, Nick

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Webgl, python script for multiple pdbs
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output. import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

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Error in using chimera with structureviz2 and cytoscape
by SRUTHI NAMBIAR 30 Jun '21

30 Jun '21

Dear all, I have been using chimera for the past 1 year and recently wanted to club it along with the cytoscape software. But whenever I try to launch chimera through the structureviz app, I get the following message: Error message: Cannot run program "/home/students/chimera/": error=13, Permission denied I have changed the settings of structureviz to give the path of chimera which is /home/students/chimera. Still this error is occurring. Could someone help regarding the same? Thank you. Regards, Sruthi

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how to calculate RMSD
by Elaine Meng 30 Jun '21

30 Jun '21

> On Jun 30, 2021, at 7:19 AM, lufeiyu(a)jlu.edu.cn wrote: > > Dear Sir/Madam: > > I have a question about the analysing of the docking. I docked a peptide to the receptor using GALAXYpepDOCK. The results uncontained the scores of RMSD. Some literatures reorted the UCSF could calculate the RMSD. But I didn't get the way after reading the tutorials. Please help me to figure out how to obtain the RMSD of a docking structure .Thanks vwry much. Best wishes for you. > > sincerely yours > Feiyu Lu Dear Feiyu Lu, The chimera-users(a)cgl.ucsf.edu address is recommended for asking questions about how to use Chimera. I CC'd it here, so you do not need to send your question again. (Or if you are using ChimeraX, you should use chimerax-users(a)cgl.ucsf.edu in the future for asking questions.) An RMSD measures the difference between two different locations of a set of atoms. So in Chimera you would need to open not only the docking results, but also the position of that peptide that you want to use as reference to calculate their RMSD. Then, you can use the "rmsd" command to compare them. I cannot give an exact command since I don't know the model numbers you will have, but an example if you had the comparison peptide open as model #3 and the docking result models are #1.1, #1.2, #1.3 ... then your commands could be: rmsd #3 #1.1 rmsd #3 #1.2 [...] See rmsd command help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> The results would be shown in the Reply Log (open from Favorites menu). Also if you don't know what model numbers you have, look in the Model Panel (also can be opened from the Favorites menu). Model Panel help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Join models function on Chimera
by Azad, Roksana 29 Jun '21

29 Jun '21

Hi There, I hope you are doing very well. My name is Roksana Azad, I am a Ph.D. Student at the CUNY ASRC. I have been working on building a full length model of my protein into a cryoEM map, I have models for individual domain but not for the full lenght structure. I am trying to join the domain models using chimera "join models" function, but unfortunately it's not working for me. I tried everything I could find online about the issue, I used the addh command and kssdssp commands and also tried joining them using other bond instead of C-N, however my button for "apply" always grey and I can't click on it (please see the screenshot attached). I also tried this command "#0:127.A@C #1:1.A@N" according to my model # and atom, but its not selecting anything for me. I tried "combine" it also didn't work.? Please let me know if there is something else I am missing or what else I can do to create this bond or connection between two models. Thank you so much for your time and help in advance - very much appreciated. Sincerely, Roksana ________________________________ Roksana Azad<https://asrc.gc.cuny.edu/people/roksana-azad/> Ph.D. Candidate in Biochemistry & Biophysics Advisor: Kevin H. Gardner<https://kglab.ws.gc.cuny.edu/> Structural Biology Initiative; CUNY Advanced Science Research Center 85 St Nicholas Terrace * New York * NY * 10031 Phone: 212-413-3233 Email: razad(a)gc.cuny.edu

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Stuck in adding residue in the C-terminal of a segment
by Prathit Chatterjee 29 Jun '21

29 Jun '21

Dear Experts, This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA. I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO. I followed the tutorial and have given the following command in command line: addaa ala,101 :100.d The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D. Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D. Thank you in advance, Regards, Prathit Chatterjee

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how to know the net charge of my system
by Sara Luz Gomez Maya 29 Jun '21

29 Jun '21

Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara

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same chain id while saving large coordinate files
by manikandank 27 Jun '21

27 Jun '21

Hi Chimera-users, Chimera 1.15 (build 42258) puts same chain id for all protein chains present in the pdb during 'save pdb/write pdb' . I am using it in linux Ubuntu. Please help. thank you with kind regards Mani.

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Modeller..Waiting for the Opal server
by Hernando J Sosa 26 Jun '21

26 Jun '21

Dear Chimera, Today when trying to use Modeller through the Chimera interface (via web service) the program either stays forever in Waiting for the Opal server or produces a whole bunch of errors. Trying to run Modeller through the local installation also results in errors. Not sure if the problem is with Chimera or Modeller but one day ago Modeller&Chimera were working fine with the same input files that now are causing the errors (???). Thanks Best Hernando

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multi align viewer
by Jacqueline Vitali 25 Jun '21

25 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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multialign viewer
by Jacqueline Vitali 23 Jun '21

23 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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Regarding problem 'During selection from the graphics window (picking)'
by Dr. Abhay Nanda Srivastava 20 Jun '21

20 Jun '21

Dear Team Chimera, I am using Chimera software in Windows 7, 32 bit computer for viewing Swiss dock prediction results. But, when I try to select the residue or atom in model by using mouse and keyboard button (Ctrl+button 1), no selection is displayed, even hand like cursor seen on the graphics, I am also not able to see the residue or atoms labeling by putting cursor on model. For my confusion removal, I have downloaded and installed the software on another computer of Windows 7, 64 bit. But here also, the same problem persists. Please suggest to me, how to get rid of this problem? Looking forward to hearing from you. Thank You. *Regards,* *Dr. Abhay N. Srivastava* * M. Sc. (Chem.), Ph. D. Head & Asst. Professor,* * Department of Chemistry,* * NC-BRA Bihar University,* * Muzaffarpur-India.* * Contact: +91-9990576112*

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Question regarding the chimera Transform Coordinates feature
by Ritwik Jain 19 Jun '21

19 Jun '21

Respected developers of chimera, I am currently doing a research project related to Cryo-EM map alignment in which I need to use Chimera. Chimera has a feature which transforms the coordinates of a molecule (Img1.jpg) . That feature has an option to move atoms instead of coordinate axes (Img2.jpg). If I uncheck that box and transform, the model just reverts back to its original position after saving and reopening. I was wondering if there was a command line command for the " move atoms instead of coordinate axes " option. I have tried all the move commands ( https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html) and they don't seem to work. I expect your reply soon. Sincerely, Ritwik Jain

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chimera installation problem
by Monojit roy 18 Jun '21

18 Jun '21

sir, please help

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AddH on N atom in N-terminal
by 陈恩博 17 Jun '21

17 Jun '21

Hello. When I use addH to add H atoms on N atom in N-terminal of Peptide chain, I find 3 H were added on this N. Why the addH result is C-NH3 and not C-NH2? Thanks!

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color maps based on real space cross correlation
by manikandank 16 Jun '21

16 Jun '21

Hi Chimera-users, I have aligned two cryoEM maps at certain threshold using 'Fit in Map' option in chimera. Now I would like to color one map based on real space voxel correlation values from 'Fit in Map' operation. Please let me know how this can be done in chimera. thank you with kind regards Mani.

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command line: how to add hydrogens to a phosphate group?
by Sara Luz Gomez Maya 15 Jun '21

15 Jun '21

Hi, I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried: labelopt info idatmType label #0 addh spec O3- but it did not work. You can find attached herewith the pdb file. Any help is appreciated. Regards, Sara

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Sending Chimera MD job to remote computer
by Cowie, Connor 14 Jun '21

14 Jun '21

Hello, I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password). However, I want to be able to send a command to a remote computer to improve the computational time especially when running multiple MD simulations; right now, I am running MD simulations on the same computer. I was first thinking of a sequence of commands below: Ctrl+Z bg ssh -y username@detroit05 I know that the Ctrl+Z command temporarily pauses a command, but I believe that the jobs command is first needed to list the current running jobs (that Ctrl+Z can be performed on). However, the running jobs are not listed when I type “jobs”. After using the “top” command to list all of the processes, I have verified that the Kill command works by typing these in succession: Kill -STOP PID# Kill -CONT PID# Can you walk me through how to first have a listing of jobs running in Chimera and then sending it to a remote computer? Best, Connor

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getting surface patches
by Diego Amaya 13 Jun '21

13 Jun '21

Hello all, I'm trying to get surface patches of PDB structures in VTK format. So I want to define a patch as the set of atoms within a given radius of a specific residue, build the surface corresponding to that patch and export the result in VTK format. Additionally, I want to do all this with a python script. Here the code I'm trying but doesn't work : *import pychimerapychimera.patch_environ()pychimera.enable_chimera()import osimport chimerafrom chimera import runCommand as rc* *list_resid = [31, 64]* *radius = 3list_pdbs = ['ensayo.pdb']for resid in list_resid: for line in list_pdbs: list_atoms = [] rc('open '+line) rc('sel :{} za<{}'.format(resid, radius)) for a in chimera.selection.currentAtoms(): list_atoms.append('serialNumber=' + str(a.serialNumber)) sel_atoms = ' or '.join(list_atoms) rc('surfcat patch @*/{}'.format(sel_atoms)) rc('surface patch') rc("export format VTK {}_resid_{}_radius_{}.vtk".format(line[:-4], resid, radius)) rc("close all")* Thanks in advance for your help. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Minimize hydrogens in water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 11 Jun '21

11 Jun '21

Hi, I need to minimize two water molecules in the binding site of the protein: I don't want to move the oxygen, so I've selected only hydrogen atoms and then I' ve used the Minimize Structure tool (keeping fixed all atoms that are unselected). I can't do the minimization because there's an error: Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.CYS_394__0_0_1_397__A.N (atom type n) - Atom 0.GLY_393__0_0_1_396__A.peptide.C (atom type C)'' I don't known what this means and what I should do to fix it. I've tried to use the command line, but there's another error. Does anyone have suggestions? Thank you. Francesca

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